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-rw-r--r--gn_auth/auth/authorisation/groups/views.py431
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diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/groups/views.py
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+"""The views/routes for the `gn3.auth.authorisation.groups` package."""
+import uuid
+import datetime
+from typing import Iterable
+from functools import partial
+
+from MySQLdb.cursors import DictCursor
+from flask import request, jsonify, Response, Blueprint, current_app
+
+from gn3.auth import db
+from gn3 import db_utils as gn3db
+
+from gn3.auth.dictify import dictify
+from gn3.auth.db_utils import with_db_connection
+
+from .data import link_data_to_group
+from .models import (
+ Group, user_group, all_groups, DUMMY_GROUP, GroupRole, group_by_id,
+ join_requests, group_role_by_id, GroupCreationError,
+ accept_reject_join_request, group_users as _group_users,
+ create_group as _create_group, add_privilege_to_group_role,
+ delete_privilege_from_group_role, create_group_role as _create_group_role)
+
+from ..roles.models import Role
+from ..roles.models import user_roles
+
+from ..checks import authorised_p
+from ..privileges import Privilege, privileges_by_ids
+from ..errors import InvalidData, NotFoundError, AuthorisationError
+
+from ...authentication.users import User
+from ...authentication.oauth2.resource_server import require_oauth
+
+groups = Blueprint("groups", __name__)
+
+@groups.route("/list", methods=["GET"])
+@require_oauth("profile group")
+def list_groups():
+ """Return the list of groups that exist."""
+ with db.connection(current_app.config["AUTH_DB"]) as conn:
+ the_groups = all_groups(conn)
+
+ return jsonify(the_groups.maybe(
+ [], lambda grps: [dictify(grp) for grp in grps]))
+
+@groups.route("/create", methods=["POST"])
+@require_oauth("profile group")
+def create_group():
+ """Create a new group."""
+ with require_oauth.acquire("profile group") as the_token:
+ group_name=request.form.get("group_name", "").strip()
+ if not bool(group_name):
+ raise GroupCreationError("Could not create the group.")
+
+ db_uri = current_app.config["AUTH_DB"]
+ with db.connection(db_uri) as conn:
+ user = the_token.user
+ new_group = _create_group(
+ conn, group_name, user, request.form.get("group_description"))
+ return jsonify({
+ **dictify(new_group), "group_leader": dictify(user)
+ })
+
+@groups.route("/members/<uuid:group_id>", methods=["GET"])
+@require_oauth("profile group")
+def group_members(group_id: uuid.UUID) -> Response:
+ """Retrieve all the members of a group."""
+ with require_oauth.acquire("profile group") as the_token:# pylint: disable=[unused-variable]
+ db_uri = current_app.config["AUTH_DB"]
+ ## Check that user has appropriate privileges and remove the pylint disable above
+ with db.connection(db_uri) as conn:
+ return jsonify(tuple(
+ dictify(user) for user in _group_users(conn, group_id)))
+
+@groups.route("/requests/join/<uuid:group_id>", methods=["POST"])
+@require_oauth("profile group")
+def request_to_join(group_id: uuid.UUID) -> Response:
+ """Request to join a group."""
+ def __request__(conn: db.DbConnection, user: User, group_id: uuid.UUID,
+ message: str):
+ with db.cursor(conn) as cursor:
+ group = user_group(conn, user).maybe(# type: ignore[misc]
+ False, lambda grp: grp)# type: ignore[arg-type]
+ if group:
+ error = AuthorisationError(
+ "You cannot request to join a new group while being a "
+ "member of an existing group.")
+ error.error_code = 400
+ raise error
+ request_id = uuid.uuid4()
+ cursor.execute(
+ "INSERT INTO group_join_requests VALUES "
+ "(:request_id, :group_id, :user_id, :ts, :status, :msg)",
+ {
+ "request_id": str(request_id),
+ "group_id": str(group_id),
+ "user_id": str(user.user_id),
+ "ts": datetime.datetime.now().timestamp(),
+ "status": "PENDING",
+ "msg": message
+ })
+ return {
+ "request_id": request_id,
+ "message": "Successfully sent the join request."
+ }
+
+ with require_oauth.acquire("profile group") as the_token:
+ form = request.form
+ results = with_db_connection(partial(
+ __request__, user=the_token.user, group_id=group_id, message=form.get(
+ "message", "I hereby request that you add me to your group.")))
+ return jsonify(results)
+
+@groups.route("/requests/join/list", methods=["GET"])
+@require_oauth("profile group")
+def list_join_requests() -> Response:
+ """List the pending join requests."""
+ with require_oauth.acquire("profile group") as the_token:
+ return jsonify(with_db_connection(partial(
+ join_requests, user=the_token.user)))
+
+@groups.route("/requests/join/accept", methods=["POST"])
+@require_oauth("profile group")
+def accept_join_requests() -> Response:
+ """Accept a join request."""
+ with require_oauth.acquire("profile group") as the_token:
+ form = request.form
+ request_id = uuid.UUID(form.get("request_id"))
+ return jsonify(with_db_connection(partial(
+ accept_reject_join_request, request_id=request_id,
+ user=the_token.user, status="ACCEPTED")))
+
+@groups.route("/requests/join/reject", methods=["POST"])
+@require_oauth("profile group")
+def reject_join_requests() -> Response:
+ """Reject a join request."""
+ with require_oauth.acquire("profile group") as the_token:
+ form = request.form
+ request_id = uuid.UUID(form.get("request_id"))
+ return jsonify(with_db_connection(partial(
+ accept_reject_join_request, request_id=request_id,
+ user=the_token.user, status="REJECTED")))
+
+def unlinked_mrna_data(
+ conn: db.DbConnection, group: Group) -> tuple[dict, ...]:
+ """
+ Retrieve all mRNA Assay data linked to a group but not linked to any
+ resource.
+ """
+ query = (
+ "SELECT lmd.* FROM linked_mrna_data lmd "
+ "LEFT JOIN mrna_resources mr ON lmd.data_link_id=mr.data_link_id "
+ "WHERE lmd.group_id=? AND mr.data_link_id IS NULL")
+ with db.cursor(conn) as cursor:
+ cursor.execute(query, (str(group.group_id),))
+ return tuple(dict(row) for row in cursor.fetchall())
+
+def unlinked_genotype_data(
+ conn: db.DbConnection, group: Group) -> tuple[dict, ...]:
+ """
+ Retrieve all genotype data linked to a group but not linked to any resource.
+ """
+ query = (
+ "SELECT lgd.* FROM linked_genotype_data lgd "
+ "LEFT JOIN genotype_resources gr ON lgd.data_link_id=gr.data_link_id "
+ "WHERE lgd.group_id=? AND gr.data_link_id IS NULL")
+ with db.cursor(conn) as cursor:
+ cursor.execute(query, (str(group.group_id),))
+ return tuple(dict(row) for row in cursor.fetchall())
+
+def unlinked_phenotype_data(
+ authconn: db.DbConnection, gn3conn: gn3db.Connection,
+ group: Group) -> tuple[dict, ...]:
+ """
+ Retrieve all phenotype data linked to a group but not linked to any
+ resource.
+ """
+ with db.cursor(authconn) as authcur, gn3conn.cursor(DictCursor) as gn3cur:
+ authcur.execute(
+ "SELECT lpd.* FROM linked_phenotype_data AS lpd "
+ "LEFT JOIN phenotype_resources AS pr "
+ "ON lpd.data_link_id=pr.data_link_id "
+ "WHERE lpd.group_id=? AND pr.data_link_id IS NULL",
+ (str(group.group_id),))
+ results = authcur.fetchall()
+ ids: dict[tuple[str, ...], str] = {
+ (
+ row["SpeciesId"], row["InbredSetId"], row["PublishFreezeId"],
+ row["PublishXRefId"]): row["data_link_id"]
+ for row in results
+ }
+ if len(ids.keys()) < 1:
+ return tuple()
+ paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(ids.keys()))
+ gn3cur.execute(
+ "SELECT spc.SpeciesId, spc.SpeciesName, iset.InbredSetId, "
+ "iset.InbredSetName, pf.Id AS PublishFreezeId, "
+ "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, "
+ "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId, "
+ "pub.PubMed_ID, pub.Title, pub.Year, "
+ "phen.Pre_publication_description, "
+ "phen.Post_publication_description, phen.Original_description "
+ "FROM "
+ "Species AS spc "
+ "INNER JOIN InbredSet AS iset "
+ "ON spc.SpeciesId=iset.SpeciesId "
+ "INNER JOIN PublishFreeze AS pf "
+ "ON iset.InbredSetId=pf.InbredSetId "
+ "INNER JOIN PublishXRef AS pxr "
+ "ON pf.InbredSetId=pxr.InbredSetId "
+ "INNER JOIN Publication AS pub "
+ "ON pxr.PublicationId=pub.Id "
+ "INNER JOIN Phenotype AS phen "
+ "ON pxr.PhenotypeId=phen.Id "
+ "WHERE (spc.SpeciesId, iset.InbredSetId, pf.Id, pxr.Id) "
+ f"IN ({paramstr})",
+ tuple(item for sublist in ids.keys() for item in sublist))
+ return tuple({
+ **{key: value for key, value in row.items() if key not in
+ ("Post_publication_description", "Pre_publication_description",
+ "Original_description")},
+ "description": (
+ row["Post_publication_description"] or
+ row["Pre_publication_description"] or
+ row["Original_description"]),
+ "data_link_id": ids[tuple(str(row[key]) for key in (
+ "SpeciesId", "InbredSetId", "PublishFreezeId",
+ "PublishXRefId"))]
+ } for row in gn3cur.fetchall())
+
+@groups.route("/<string:resource_type>/unlinked-data")
+@require_oauth("profile group resource")
+def unlinked_data(resource_type: str) -> Response:
+ """View data linked to the group but not linked to any resource."""
+ if resource_type not in ("all", "mrna", "genotype", "phenotype"):
+ raise AuthorisationError(f"Invalid resource type {resource_type}")
+
+ with require_oauth.acquire("profile group resource") as the_token:
+ db_uri = current_app.config["AUTH_DB"]
+ gn3db_uri = current_app.config["SQL_URI"]
+ with (db.connection(db_uri) as authconn,
+ gn3db.database_connection(gn3db_uri) as gn3conn):
+ ugroup = user_group(authconn, the_token.user).maybe(# type: ignore[misc]
+ DUMMY_GROUP, lambda grp: grp)
+ if ugroup == DUMMY_GROUP:
+ return jsonify(tuple())
+
+ unlinked_fns = {
+ "mrna": unlinked_mrna_data,
+ "genotype": unlinked_genotype_data,
+ "phenotype": lambda conn, grp: partial(
+ unlinked_phenotype_data, gn3conn=gn3conn)(
+ authconn=conn, group=grp)
+ }
+ return jsonify(tuple(
+ dict(row) for row in unlinked_fns[resource_type](
+ authconn, ugroup)))
+
+ return jsonify(tuple())
+
+@groups.route("/data/link", methods=["POST"])
+@require_oauth("profile group resource")
+def link_data() -> Response:
+ """Link selected data to specified group."""
+ with require_oauth.acquire("profile group resource") as _the_token:
+ form = request.form
+ group_id = uuid.UUID(form["group_id"])
+ dataset_ids = form.getlist("dataset_ids")
+ dataset_type = form.get("dataset_type")
+ if dataset_type not in ("mrna", "genotype", "phenotype"):
+ raise InvalidData("Unexpected dataset type requested!")
+ def __link__(conn: db.DbConnection):
+ group = group_by_id(conn, group_id)
+ with gn3db.database_connection(current_app.config["SQL_URI"]) as gn3conn:
+ return link_data_to_group(
+ conn, gn3conn, dataset_type, dataset_ids, group)
+
+ return jsonify(with_db_connection(__link__))
+
+@groups.route("/roles", methods=["GET"])
+@require_oauth("profile group")
+def group_roles():
+ """Return a list of all available group roles."""
+ with require_oauth.acquire("profile group role") as the_token:
+ def __list_roles__(conn: db.DbConnection):
+ ## TODO: Check that user has appropriate privileges
+ with db.cursor(conn) as cursor:
+ group = user_group(conn, the_token.user).maybe(# type: ignore[misc]
+ DUMMY_GROUP, lambda grp: grp)
+ if group == DUMMY_GROUP:
+ return tuple()
+ cursor.execute(
+ "SELECT gr.group_role_id, r.* "
+ "FROM group_roles AS gr INNER JOIN roles AS r "
+ "ON gr.role_id=r.role_id "
+ "WHERE group_id=?",
+ (str(group.group_id),))
+ return tuple(
+ GroupRole(uuid.UUID(row["group_role_id"]),
+ group,
+ Role(uuid.UUID(row["role_id"]),
+ row["role_name"],
+ bool(int(row["user_editable"])),
+ tuple()))
+ for row in cursor.fetchall())
+ return jsonify(tuple(
+ dictify(role) for role in with_db_connection(__list_roles__)))
+
+@groups.route("/privileges", methods=["GET"])
+@require_oauth("profile group")
+def group_privileges():
+ """Return a list of all available group roles."""
+ with require_oauth.acquire("profile group role") as the_token:
+ def __list_privileges__(conn: db.DbConnection) -> Iterable[Privilege]:
+ ## TODO: Check that user has appropriate privileges
+ this_user_roles = user_roles(conn, the_token.user)
+ with db.cursor(conn) as cursor:
+ cursor.execute("SELECT * FROM privileges "
+ "WHERE privilege_id LIKE 'group:%'")
+ group_level_roles = tuple(
+ Privilege(row["privilege_id"], row["privilege_description"])
+ for row in cursor.fetchall())
+ return tuple(privilege for arole in this_user_roles
+ for privilege in arole.privileges) + group_level_roles
+ return jsonify(tuple(
+ dictify(priv) for priv in with_db_connection(__list_privileges__)))
+
+
+
+@groups.route("/role/create", methods=["POST"])
+@require_oauth("profile group")
+def create_group_role():
+ """Create a new group role."""
+ with require_oauth.acquire("profile group role") as the_token:
+ ## TODO: Check that user has appropriate privileges
+ @authorised_p(("group:role:create-role",),
+ "You do not have the privilege to create new roles",
+ oauth2_scope="profile group role")
+ def __create__(conn: db.DbConnection) -> GroupRole:
+ ## TODO: Check user cannot assign any privilege they don't have.
+ form = request.form
+ role_name = form.get("role_name", "").strip()
+ privileges_ids = form.getlist("privileges[]")
+ if len(role_name) == 0:
+ raise InvalidData("Role name not provided!")
+ if len(privileges_ids) == 0:
+ raise InvalidData(
+ "At least one privilege needs to be provided.")
+
+ group = user_group(conn, the_token.user).maybe(# type: ignore[misc]
+ DUMMY_GROUP, lambda grp: grp)
+
+ if group == DUMMY_GROUP:
+ raise AuthorisationError(
+ "A user without a group cannot create a new role.")
+ privileges = privileges_by_ids(conn, tuple(privileges_ids))
+ if len(privileges_ids) != len(privileges):
+ raise InvalidData(
+ f"{len(privileges_ids) - len(privileges)} of the selected "
+ "privileges were not found in the database.")
+
+ return _create_group_role(conn, group, role_name, privileges)
+
+ return jsonify(with_db_connection(__create__))
+
+@groups.route("/role/<uuid:group_role_id>", methods=["GET"])
+@require_oauth("profile group")
+def view_group_role(group_role_id: uuid.UUID):
+ """Return the details of the given role."""
+ with require_oauth.acquire("profile group role") as the_token:
+ def __group_role__(conn: db.DbConnection) -> GroupRole:
+ group = user_group(conn, the_token.user).maybe(#type: ignore[misc]
+ DUMMY_GROUP, lambda grp: grp)
+
+ if group == DUMMY_GROUP:
+ raise AuthorisationError(
+ "A user without a group cannot view group roles.")
+ return group_role_by_id(conn, group, group_role_id)
+ return jsonify(dictify(with_db_connection(__group_role__)))
+
+def __add_remove_priv_to_from_role__(conn: db.DbConnection,
+ group_role_id: uuid.UUID,
+ direction: str,
+ user: User) -> GroupRole:
+ assert direction in ("ADD", "DELETE")
+ group = user_group(conn, user).maybe(# type: ignore[misc]
+ DUMMY_GROUP, lambda grp: grp)
+
+ if group == DUMMY_GROUP:
+ raise AuthorisationError(
+ "You need to be a member of a group to edit roles.")
+ try:
+ privilege_id = request.form.get("privilege_id", "")
+ assert bool(privilege_id), "Privilege to add must be provided."
+ privileges = privileges_by_ids(conn, (privilege_id,))
+ if len(privileges) == 0:
+ raise NotFoundError("Privilege not found.")
+ dir_fns = {
+ "ADD": add_privilege_to_group_role,
+ "DELETE": delete_privilege_from_group_role
+ }
+ return dir_fns[direction](
+ conn,
+ group_role_by_id(conn, group, group_role_id),
+ privileges[0])
+ except AssertionError as aerr:
+ raise InvalidData(aerr.args[0]) from aerr
+
+@groups.route("/role/<uuid:group_role_id>/privilege/add", methods=["POST"])
+@require_oauth("profile group")
+def add_priv_to_role(group_role_id: uuid.UUID) -> Response:
+ """Add privilege to group role."""
+ with require_oauth.acquire("profile group role") as the_token:
+ return jsonify({
+ **dictify(with_db_connection(partial(
+ __add_remove_priv_to_from_role__, group_role_id=group_role_id,
+ direction="ADD", user=the_token.user))),
+ "description": "Privilege added successfully"
+ })
+
+@groups.route("/role/<uuid:group_role_id>/privilege/delete", methods=["POST"])
+@require_oauth("profile group")
+def delete_priv_from_role(group_role_id: uuid.UUID) -> Response:
+ """Delete privilege from group role."""
+ with require_oauth.acquire("profile group role") as the_token:
+ return jsonify({
+ **dictify(with_db_connection(partial(
+ __add_remove_priv_to_from_role__, group_role_id=group_role_id,
+ direction="DELETE", user=the_token.user))),
+ "description": "Privilege deleted successfully"
+ })